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基本情報
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タイトル | Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Dbp10-3 | |||||||||
![]() | local_resolution filtered map | |||||||||
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![]() | Ribosome / Ribosome biogenesis / pre-60S ribosome | |||||||||
機能・相同性 | ![]() Noc1p-Noc2p complex / Noc2p-Noc3p complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / intracellular mRNA localization / protein N-linked glycosylation via asparagine ...Noc1p-Noc2p complex / Noc2p-Noc3p complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / intracellular mRNA localization / protein N-linked glycosylation via asparagine / PeBoW complex / tRNA methylation / rRNA base methylation / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process / maturation of 5.8S rRNA / ribosomal large subunit binding / preribosome, large subunit precursor / DNA replication initiation / mRNA transport / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / translation initiation factor activity / ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / nuclear periphery / post-translational protein modification / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / cytosolic ribosome assembly / ribosomal large subunit biogenesis / rRNA processing / transcription corepressor activity / ribosome biogenesis / histone binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / negative regulation of translation / ribosome / RNA helicase / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / chromatin binding / nucleolus / GTP binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.1 Å | |||||||||
![]() | Lau B / Huang Z / Beckmann R / Hurt E / Cheng J | |||||||||
資金援助 | 1件
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![]() | ![]() タイトル: Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis. 著者: Benjamin Lau / Zixuan Huang / Nikola Kellner / Shuangshuang Niu / Otto Berninghausen / Roland Beckmann / Ed Hurt / Jingdong Cheng / ![]() ![]() 要旨: Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ...Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ribosomal RNA is incorporated into the developing pre-60S ribosome, which in humans links ribosome biogenesis to cell proliferation by surveillance by factors such as p53-MDM2, is poorly understood. Here, we report nine nucleolar pre-60S cryo-EM structures from Chaetomium thermophilum, one of which clarifies the mechanism of 5S RNP incorporation into the early pre-60S. Successive assembly states then represent how helicases Dbp10 and Spb4, and the Pumilio domain factor Puf6 act in series to surveil the gradual folding of the nearby 25S rRNA domain IV. Finally, the methyltransferase Spb1 methylates a universally conserved guanine nucleotide in the A-loop of the peptidyl transferase center, thereby licensing further maturation. Our findings provide insight into the hierarchical action of helicases in safeguarding rRNA tertiary structure folding and coupling to surveillance mechanisms that culminate in local RNA modification. | |||||||||
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構造の表示
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 162.6 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 88.7 KB 88.7 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 14.8 KB | 表示 | ![]() |
画像 | ![]() | 123.3 KB | ||
その他 | ![]() ![]() ![]() | 248.4 MB 225.7 MB 225.8 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 964.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 964.4 KB | 表示 | |
XML形式データ | ![]() | 22.6 KB | 表示 | |
CIF形式データ | ![]() | 30.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 8i9wMC ![]() 8i9pC ![]() 8i9rC ![]() 8i9tC ![]() 8i9vC ![]() 8i9xC ![]() 8i9yC ![]() 8i9zC ![]() 8ia0C M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||
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注釈 | local_resolution filtered map | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.045 Å | ||||||||||||||||||||
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: DeepEMhancer filtered map
ファイル | emd_35286_additional_1.map | ||||||||||||
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注釈 | DeepEMhancer filtered map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_35286_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_35286_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : pre-60S ribosome
+超分子 #1: pre-60S ribosome
+超分子 #2: ribosome
+分子 #1: RNA (3341-MER)
+分子 #2: RNA (319-MER)
+分子 #3: Brix domain-containing protein
+分子 #4: Ribosome biogenesis protein C8F11.04
+分子 #5: Ribosome biogenesis protein ERB1
+分子 #6: RNA helicase
+分子 #7: Ribosome assembly factor mrt4
+分子 #8: 60S ribosome subunit biogenesis protein NIP7
+分子 #9: Nucleolar GTP-binding protein 1
+分子 #10: Putative RNA-binding protein
+分子 #11: Pescadillo homolog
+分子 #12: Ribosome biogenesis protein NSA2 homolog
+分子 #13: Putative GTP binding protein
+分子 #14: 60S ribosomal protein l7-like protein
+分子 #15: Eukaryotic translation initiation factor 6
+分子 #16: DUF2423 domain-containing protein
+分子 #17: RNA methyltransferase nop2-like protein
+分子 #18: Ribosome biogenesis protein RLP24
+分子 #19: Nucleolar protein 16
+分子 #20: AdoMet-dependent rRNA methyltransferase SPB1
+分子 #21: Nucleolar complex-associated protein 3
+分子 #22: rRNA-processing protein EBP2
+分子 #23: Putative 60S ribosomal protein
+分子 #24: 60S ribosomal subunit-like protein
+分子 #25: Putative NOC2 family protein
+分子 #26: ATP-dependent RNA helicase DBP10
+分子 #27: rRNA-processing protein
+分子 #28: 60S ribosomal protein L3-like protein
+分子 #29: 60S ribosomal protein L4-like protein
+分子 #30: 60S ribosomal protein L6
+分子 #31: 60S ribosomal protein L8
+分子 #32: 60S ribosomal protein l9-like protein
+分子 #33: 60S ribosomal protein L12-like protein
+分子 #34: 60S ribosomal protein L13
+分子 #35: 60S ribosomal protein L14-like protein
+分子 #36: Ribosomal protein L15
+分子 #37: 60S ribosomal protein L16-like protein
+分子 #38: 60S ribosomal protein l17-like protein
+分子 #39: Ribosomal protein L18-like protein
+分子 #40: 60S ribosomal protein L20
+分子 #41: 60S ribosomal protein l21-like protein
+分子 #42: 60S ribosomal protein l23-like protein
+分子 #43: 60S ribosomal protein L25-like protein
+分子 #44: 60S ribosomal protein L26-like protein
+分子 #45: Putative 60S ribosomal protein
+分子 #46: 60S ribosomal protein L32-like protein
+分子 #47: 60S ribosomal protein l33-like protein
+分子 #48: dolichyl-diphosphooligosaccharide--protein glycotransferase
+分子 #49: 60S ribosomal protein L36
+分子 #50: Ribosomal protein L37
+分子 #51: Ribosomal protein
+分子 #52: GUANOSINE-5'-TRIPHOSPHATE
+分子 #53: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.4 |
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凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均電子線量: 44.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 0.8 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |